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Sample Info

single cell RNAseq

single end

non-stranded

50 bp reads

Drosophila

QA/QC

Coverage

Percentage of mitochondrial genes

GFP expression

Detected gene

count >= 1

Coverage vs Detected gene

Commonly detected gene

Expression level

expression of detected genes (count>=1)

Filter

Filter sample

Mapped reads >= 1 million

Percentage of mitochondrial genes <= 10%

Detected gene >= 4000

Filter gene

This is depends on how rare the sub-population we are looking for. Here we hope the population are more than 5 cells. Commonly expressed gene (count>=5) in cells >=5 and <= (total cell - 5)

Use protein coding gene only for downstream analysis.

ERCC correlation after filtering

Correlation after filtering

PCA after filtering

Normalization

use RUV package

Correlation after normalization

PCA after normalization

Marker gene expression

Expression table

Expression table

Clustering

Heatmap

DE genes

Trajectory analysis